Run alleleCount

The alleleCount program primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenberg.

Usage

allele_counter(
  hts_file,
  loci_file,
  ofile,
  ...,
  odir = getwd(),
  alleleCounter = NULL
)

Arguments

hts_file

A string of path to sample HTS file.

loci_file

A string of path to loci file.

ofile

A string of path to the output file.

...

<dynamic dots> Additional arguments passed to alleleCounter command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using shQuote(). Details see: cmd_help(alleleCounter()).

odir

A string of path to the output directory.

alleleCounter

A string of path to alleleCounter command.

Value

A command object.

See also

• https://github.com/cancerit/alleleCount

• cmd_wd()/cmd_envvar()/cmd_envpath()/cmd_condaenv()

• cmd_on_start()/cmd_on_exit()

• cmd_on_succeed()/cmd_on_fail()

• cmd_parallel()

Other commands: bcftools(), bedtools(), bowtie2(), bwa(), cellranger(), conda(), fastp(), fastq_pair(), freebayes(), gistic2(), kraken2(), kraken_tools(), minimap2(), perl(), pyscenic(), python(), samtools(), seqkit(), snpEff(), strelka(), trust4(), varscan()